The files you upload at Savannah needs to be created / editable using
free software, and the free replacements need to be at least as good as
the proprietary one.

In the case of Gnash, it's currently not fast enough. Until the Cairo
backend is done, it essentially requires a 3D card, which nowadays
almost always run with proprietary software only; this is a non-trivial
issue.

If your particular Flash file plays as well with Gnash than with
Macromedia/Adobe Flash, there's no problem with uploading it at
Savannah. In the opposite case, you're essentially enticing users to use
Adobe Flash for a decent "user experience", so that's not a good value
to promote.